Variant report

Variant	rs62395244
Chromosome Location	chr6:11731682-11731683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr6:11730225-11733592	GM12878	blood:	n/a	n/a
2	STAT5A	chr6:11731588-11733345	GM12878	blood:	n/a	chr6:11732990-11733002 chr6:11732311-11732322
3	FOXA2	chr6:11731663-11731947	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:11730789-11732044	GM19193	blood:	n/a	n/a
5	POLR2A	chr6:11730546-11733461	GM12878	blood:	n/a	n/a
6	FOXA1	chr6:11731667-11732053	HepG2	liver:	n/a	n/a
7	HNF4A	chr6:11731675-11731951	HepG2	liver:	n/a	chr6:11731801-11731814 chr6:11731831-11731846 chr6:11731801-11731813 chr6:11731801-11731814 chr6:11731799-11731814 chr6:11731801-11731814 chr6:11731828-11731850 chr6:11731800-11731813 chr6:11731801-11731813
8	POLR2A	chr6:11730647-11733571	GM12892	blood:	n/a	n/a
9	POLR2A	chr6:11730690-11733720	GM12892	blood:	n/a	n/a
10	NFIC	chr6:11731457-11733009	GM12878	blood:	n/a	chr6:11732741-11732758
11	MTA3	chr6:11730668-11733834	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:11730777-11732117	GM12891	blood:	n/a	n/a
13	POLR2A	chr6:11730360-11733534	GM12878	blood:	n/a	n/a
14	PML	chr6:11730451-11733512	GM12878	blood:	n/a	n/a
15	NFIC	chr6:11730485-11733613	GM12878	blood:	n/a	chr6:11732741-11732758
16	POLR2A	chr6:11730712-11732317	GM12892	blood:	n/a	n/a
17	POLR2A	chr6:11730715-11732098	GM12892	blood:	n/a	n/a
18	HNF4G	chr6:11731579-11732037	HepG2	liver:	n/a	chr6:11731800-11731815 chr6:11731801-11731814 chr6:11731801-11731813 chr6:11731801-11731814 chr6:11731801-11731814 chr6:11731828-11731850 chr6:11731800-11731813 chr6:11731801-11731813
19	FOXA1	chr6:11731665-11732029	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:11730703-11732153	GM12891	blood:	n/a	n/a
21	NFATC1	chr6:11730673-11733185	GM12878	blood:	n/a	n/a
22	HNF4G	chr6:11731655-11731938	HepG2	liver:	n/a	chr6:11731800-11731815 chr6:11731801-11731814 chr6:11731801-11731813 chr6:11731801-11731814 chr6:11731801-11731814 chr6:11731828-11731850 chr6:11731800-11731813 chr6:11731801-11731813
23	FOXM1	chr6:11731616-11733044	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:11730836-11733271	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:11722035..11725191-chr6:11730801..11735491,4	K562	blood:
2	chr6:11726535..11729461-chr6:11731362..11733356,2	MCF-7	breast:
3	chr6:11729664..11733352-chr6:11734064..11737412,4	K562	blood:
4	chr6:11728883..11730943-chr6:11731032..11732727,2	K562	blood:

Variant related genes	Relation type
ADTRP	TF binding region
ENSG00000111863	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17401908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17402850	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17480980	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62395242	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62395243	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62395245	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62395247	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv428470	chr6:11686198-11747850	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462637	chr6:11710554-11733777	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv600990	chr6:11710554-11733777	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11711600-11731800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:11719400-11762200	Weak transcription	Colonic Mucosa	Colon
3	chr6:11719600-11732400	Weak transcription	NHEK	skin
4	chr6:11723200-11732400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:11723200-11738400	Weak transcription	HMEC	breast
6	chr6:11723600-11744200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:11725200-11748600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:11726400-11744600	Weak transcription	Right Atrium	heart
9	chr6:11727000-11734000	Enhancers	Primary hematopoietic stem cells	blood
10	chr6:11727600-11731800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:11727800-11732800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:11728800-11732400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:11729000-11733000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:11729200-11732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:11729200-11732600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:11729400-11732200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:11729400-11733200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:11729400-11733200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr6:11729600-11733200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:11729600-11734000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:11729800-11731800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:11729800-11733200	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr6:11730000-11732400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr6:11730000-11732600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:11730200-11736200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:11730400-11731800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr6:11730600-11731800	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr6:11730600-11732400	Enhancers	Primary T cells fromperipheralblood	blood
29	chr6:11730600-11733200	Enhancers	Fetal Thymus	thymus
30	chr6:11730800-11731800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr6:11730800-11733400	Enhancers	Adipose Nuclei	Adipose
32	chr6:11731000-11731800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:11731000-11731800	Weak transcription	Aorta	Aorta
34	chr6:11731000-11732200	Enhancers	Primary B cells from cord blood	blood
35	chr6:11731000-11732400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:11731000-11732400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:11731000-11732400	Enhancers	Fetal Intestine Large	intestine
38	chr6:11731000-11732400	Enhancers	Fetal Intestine Small	intestine
39	chr6:11731000-11732400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr6:11731000-11732600	Enhancers	Psoas Muscle	Psoas
41	chr6:11731000-11733200	Enhancers	Gastric	stomach
42	chr6:11731200-11731800	Weak transcription	Primary T cells from cord blood	blood
43	chr6:11731200-11731800	Enhancers	Brain Substantia Nigra	brain
44	chr6:11731200-11732000	Enhancers	Spleen	Spleen
45	chr6:11731200-11732400	Weak transcription	Esophagus	oesophagus
46	chr6:11731200-11732600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:11731200-11732600	Enhancers	Right Ventricle	heart
48	chr6:11731200-11733000	Flanking Active TSS	GM12878-XiMat	blood
49	chr6:11731200-11733200	Enhancers	Pancreas	Pancrea
50	chr6:11731400-11732200	Enhancers	Liver	Liver

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